Nothing is of course impossible in the world of software, but no – I don’t think it’s possible that this is the cause here.
You’re not going to like this, but I’m fairly sure that you in fact are not entering the right password.
What might confuse you a little bit is that when you upgrade, you’ll first be asked to set a new password for your account. Then, when you open an AxCrypt 1.x file the first time, it’ll ask you for the original password you used with AxCrypt 1 for the file. If you enter it correctly, the file will automatically be re-encrypted with version 2, and use the new sign in password for AxCrypt 2.